/dports/biology/hisat2/hisat2-2.2.1/li_hla/ |
H A D | alignments.hpp | 195 if ( !bam_aux_get( b, "CC" ) || !bam_aux_get( b, "CP" ) ) in GetRepeatPosition() 202 std::string s( bam_aux2Z( bam_aux_get(b, "CC" ) ) ) ; in GetRepeatPosition() 204 pos = bam_aux2i( bam_aux_get( b, "CP" ) ) ;// Possible error for 64bit in GetRepeatPosition() 229 if ( bam_aux_get( b, "NH" ) ) in IsUnique() 231 if ( bam_aux2i( bam_aux_get( b, "NH" ) ) > 1 ) in IsUnique() 239 if ( bam_aux_get( b, f ) ) in GetFieldI() 241 return bam_aux2i( bam_aux_get( b, f ) ) ; in GetFieldI() 248 if ( bam_aux_get( b, f ) ) in GetFieldZ() 250 return bam_aux2Z( bam_aux_get( b, f ) ) ; in GetFieldZ() 260 if ( bam_aux_get( b, "XS" ) ) in GetStrand() [all …]
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/dports/biology/vt/vt-0.57721/lib/htslib/test/ |
H A D | sam.c | 61 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get() 140 if (bam_aux_get(aln,"XA")) in aux_fields1() 202 if ((p = bam_aux_get(aln, "Y2")) && bam_aux2i(p) != -2147483647) in aux_fields1() 205 if ((p = bam_aux_get(aln, "Y3")) && bam_aux2i(p) != -1) in aux_fields1() 208 if ((p = bam_aux_get(aln, "Y4")) && bam_aux2i(p) != 0) in aux_fields1() 211 if ((p = bam_aux_get(aln, "Y5")) && bam_aux2i(p) != 1) in aux_fields1() 214 if ((p = bam_aux_get(aln, "Y6")) && bam_aux2i(p) != 2147483647) in aux_fields1() 217 if ((p = bam_aux_get(aln, "Y7")) && bam_aux2i(p) != 2147483648LL) in aux_fields1() 220 if ((p = bam_aux_get(aln, "Y8")) && bam_aux2i(p) != 4294967295LL) in aux_fields1() 227 if ((p = bam_aux_get(aln, "N0")) && bam_aux2i(p) != ival) in aux_fields1() [all …]
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/test/ |
H A D | sam.c | 61 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get() 140 if (bam_aux_get(aln,"XA")) in aux_fields1() 202 if ((p = bam_aux_get(aln, "Y2")) && bam_aux2i(p) != -2147483647) in aux_fields1() 205 if ((p = bam_aux_get(aln, "Y3")) && bam_aux2i(p) != -1) in aux_fields1() 208 if ((p = bam_aux_get(aln, "Y4")) && bam_aux2i(p) != 0) in aux_fields1() 211 if ((p = bam_aux_get(aln, "Y5")) && bam_aux2i(p) != 1) in aux_fields1() 214 if ((p = bam_aux_get(aln, "Y6")) && bam_aux2i(p) != 2147483647) in aux_fields1() 217 if ((p = bam_aux_get(aln, "Y7")) && bam_aux2i(p) != 2147483648LL) in aux_fields1() 220 if ((p = bam_aux_get(aln, "Y8")) && bam_aux2i(p) != 4294967295LL) in aux_fields1() 227 if ((p = bam_aux_get(aln, "N0")) && bam_aux2i(p) != ival) in aux_fields1() [all …]
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/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
H A D | bam_color.c | 14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_md.c | 89 uint8_t *old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core() 101 uint8_t *old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core() 121 uint8_t *q = bam_aux_get(b, "RG"); in bam_fillmd1_core() 198 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core() 199 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
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/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
H A D | bam_color.c | 14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_md.c | 89 uint8_t *old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core() 101 uint8_t *old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core() 121 uint8_t *q = bam_aux_get(b, "RG"); in bam_fillmd1_core() 198 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core() 199 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
H A D | bam_color.c | 14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_md.c | 80 old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core() 90 old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core() 174 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core() 175 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_color.c | 42 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 71 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 129 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_color.c.pysam.c | 44 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 73 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 131 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_fastq.c | 636 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index() 638 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index() 645 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index() 647 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index() 707 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 713 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 804 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
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H A D | bam_fastq.c.pysam.c | 638 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index() 640 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index() 647 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index() 649 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index() 709 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 715 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 806 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
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H A D | bam_mate.c | 73 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar() 74 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar() 189 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc() 198 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc() 245 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
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H A D | bam_mate.c.pysam.c | 75 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar() 76 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar() 191 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc() 200 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc() 247 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
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H A D | bam_markdup.c | 338 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score() 383 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template() 500 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence() 967 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates() 1001 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag() 1002 || bam_aux_get(b, "XA")) { in optical_retag() 1073 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original() 1099 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original() 1517 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates() 1521 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
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H A D | bam_markdup.c.pysam.c | 340 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score() 385 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template() 502 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence() 969 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates() 1003 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag() 1004 || bam_aux_get(b, "XA")) { in optical_retag() 1075 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original() 1101 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original() 1519 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates() 1523 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_color.c | 42 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi() 71 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi() 129 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
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H A D | bam_fastq.c | 636 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index() 638 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index() 645 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index() 647 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index() 707 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 713 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec() 804 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
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H A D | bam_mate.c | 73 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar() 74 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar() 189 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc() 198 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc() 245 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
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H A D | bam_markdup.c | 338 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score() 383 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template() 500 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence() 967 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates() 1001 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag() 1002 || bam_aux_get(b, "XA")) { in optical_retag() 1073 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original() 1099 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original() 1517 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates() 1521 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
H A D | sam.c | 80 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get() 141 p = bam_aux_get(aln, target_id); in test_update_int() 155 p = bam_aux_get(aln, next_id); in test_update_int() 197 p = bam_aux_get(aln, target_id); in test_update_array() 222 p = bam_aux_get(aln, next_id); in test_update_array() 289 if (bam_aux_get(aln,"XA")) in aux_fields1() 399 p = bam_aux_get(aln, "N2"); in aux_fields1() 405 p = bam_aux_get(aln, "N3"); in aux_fields1() 422 p = bam_aux_get(aln, "F1"); in aux_fields1() 432 p = bam_aux_get(aln, "F2"); in aux_fields1() [all …]
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/dports/biology/htslib/htslib-1.14/test/ |
H A D | sam.c | 80 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get() 141 p = bam_aux_get(aln, target_id); in test_update_int() 155 p = bam_aux_get(aln, next_id); in test_update_int() 197 p = bam_aux_get(aln, target_id); in test_update_array() 222 p = bam_aux_get(aln, next_id); in test_update_array() 289 if (bam_aux_get(aln,"XA")) in aux_fields1() 399 p = bam_aux_get(aln, "N2"); in aux_fields1() 405 p = bam_aux_get(aln, "N3"); in aux_fields1() 422 p = bam_aux_get(aln, "F1"); in aux_fields1() 432 p = bam_aux_get(aln, "F2"); in aux_fields1() [all …]
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/dports/biology/star/STAR-2.7.9a/source/ |
H A D | signalFromBAM.cpp | 22 uint8_t* aNHp=bam_aux_get(bamA,"NH"); in signalFromBAM() 142 uint8_t* aNHp=bam_aux_get(bamA,"NH"); in signalFromBAM() 148 … aNH=bam_aux2i(bam_aux_get(bamA,"NH")); //write a safer function allowing for lacking NH tag in signalFromBAM()
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/dports/biology/vt/vt-0.57721/ |
H A D | augmented_bam_record.cpp | 66 ((md_aux=bam_aux_get(s, "MD")) && (md = bam_aux2Z(md_aux))); in initialize() 380 (aux=bam_aux_get(s, "MD")) && (md = bam_aux2Z(aux)); in print() 414 (aux=bam_aux_get(s, "NM")) && (nm = bam_aux2i(aux)); in print()
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